Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Ontology::SimpleGOEngine::GraphAdaptor - Graph adaptor for Bio::Ontology::SimpleGOEngine

SYNOPSIS

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  use Bio::Ontology::SimpleGOEngine::GraphAdaptor;

  my $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor;

DESCRIPTION

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This is a think adaptor to simplify use of the old and new versions of the standard CPAN Graph module (old is versions 0.2x; new is 0.5x and beyond) within Bio::Ontology::SimpleGOEngine.

This module implements only those Graph methods used by SimpleGOEngine. It is far from a complete compatibility layer! It also implements workarounds for cerain performance problems in the current versions of Graph v0.5x.

This class provides a 'new' method that determines which version of Graph is available. The object returned by 'new' is blessed into this class if the new version of Graph is available, else into the subclass

  Bio::Ontology::SimpleGOEngine::GraphAdaptor02

This class provides implementations for the required graph methods using the new version of Graph. In most cases, these are simple pass-throughs. Methods that differ in v0.2x are implemented in the subclass.

The methods implemented here or in the subclasses are listed below. In all cases, we implemented the Graph v0.5x interface. Consult the Graph v0.5x man page for details.

  add_vertex
  has_vertex
  add_edge
  has_edge
  vertices
  edges
  edges_at
  predecessors
  successors
  set_vertex_attribute
  get_vertex_attribute
  set_edge_attribute
  get_edge_attribute
  source_vertices
  sink_vertices

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Nat Goodman

Email: natg at shore.net

Address:

  Institute for Systems Biology
  1441 N 34th St
  Seattle, WA 98103-8904

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $graph = Bio::Ontology::SimpleGOEngine::GraphAdaptor->new()
 Function: Creates a new graph
 Returns : Bio::Ontology::SimpleGOEngine::GraphAdaptor02 or 
           Bio::Ontology::SimpleGOEngine::GraphAdaptor05 object, 
           depending on which Graph version is available
 Args    : none

_graph

 Title   : _graph
 Usage   : $self->_graph();
 Function: Internal method to access 'real' graph
 Returns : Graph::Directed object 
 Args    : none

_vertex_attributes

 Title   : _vertex_attributes
 Usage   : $self->vertex_attributes();
 Function: Internal method to access HASH used to store vertex attributes
 Returns : Graph::Directed object 
 Args    : none

_edge_attributes

 Title   : _edge_attributes
 Usage   : $self->edge_attributes();
 Function: Internal method to access HASH used to store edge attributes
 Returns : Graph::Directed object 
 Args    : none

_vertex2attributes

 Title   : _vertex2attributes
 Usage   : $value=$graph->_vertex2attributes($v_->{ATTRIBUTE};
           $graph->_vertex2attributes($v)->{ATTRIBUTE}=$value;
 Function: Internal method to access attributes for a specific vertex
 Returns : HASH
 Args    : none

_edge2attributes

 Title   : _edge2attributes
 Usage   : $value=$graph->_edge2attributes($u,$v)->{ATTRIBUTE};
           $graph->_edge2attributes($u,$v)->{ATTRIBUTE}=$value;
 Function: Internal method to access HASH used to store edge attributes
 Returns : HASH
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
# $Id: GraphAdaptor.pm 10525 2006-09-26 22:03:22Z sendu $
#
# BioPerl Graph adaptor for Bio::Ontology::SimpleGOEngine
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Nat Goodman <natg at shore.net>
#
# (c) Nathan Goodman natg@shore.net 2005
# (c) ISB, Institute for Systems Biology 2005
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


# Let the code begin...

package Bio::Ontology::SimpleGOEngine::GraphAdaptor;

use Graph::Directed;

use strict;
use Bio::Ontology::SimpleGOEngine::GraphAdaptor02;

use base qw(Bio::Root::Root);


sub new {
  my( $class ) = @_;
  $class = ref $class || $class;

  my $self=
    ( defined $Graph::VERSION && $Graph::VERSION >= 0.5 ) ?
      bless ( {}, $class ) :
	bless ( {}, 'Bio::Ontology::SimpleGOEngine::GraphAdaptor02' );
  $self->{_graph}=new Graph::Directed;
  $self->{_vertex_attributes}={};
  $self->{_edge_attributes}={};
  return $self;
}

# Here are the main methods

sub add_vertex {
  my $self=shift;
  $self->_graph->add_vertex(@_);
}
sub has_vertex {
  my $self=shift;
  $self->_graph->has_vertex(@_);
}
sub add_edge {
  my $self=shift;
  $self->_graph->add_edge(@_);
}
sub has_edge {
  my $self=shift;
  $self->_graph->has_edge(@_);
}
sub vertices {
  my $self=shift;
  $self->_graph->vertices(@_);
}
sub edges {
  my $self=shift;
  $self->_graph->edges(@_);
}
sub edges_at {
  my $self=shift;
  $self->_graph->edges_at(@_);
}
sub predecessors {
  my $self=shift;
  $self->_graph->predecessors(@_);
} 
sub successors {
  my $self=shift;
  $self->_graph->successors(@_);
}
sub source_vertices {
  my $self=shift;
  $self->_graph->source_vertices();
}
sub sink_vertices {
  my $self=shift;
  $self->_graph->sink_vertices();
}
# The following methods workaround a performance problem in Graph v0.5x 
# when attributes are attached to the graph
sub set_vertex_attribute {
  my($self,$v,$attribute,$value)=@_;
  $self->_vertex2attributes($v)->{$attribute}=$value;
}
sub get_vertex_attribute {
  my($self,$v,$attribute)=@_;
  $self->_vertex2attributes($v)->{$attribute};
}
sub set_edge_attribute {
  my($self,$u,$v,$attribute,$value)=@_;
  $self->_edge2attributes($u,$v)->{$attribute}=$value;
}
sub get_edge_attribute {
  my($self,$u,$v,$attribute)=@_;
  $self->_edge2attributes($u,$v)->{$attribute};
}


sub _graph {$_[0]->{_graph}; }


sub _vertex_attributes {$_[0]->{_vertex_attributes}; }


sub _edge_attributes {$_[0]->{_edge_attributes}; }


sub _vertex2attributes {
  my($self,$vertex)=@_;
  $self->_vertex_attributes->{$vertex} or $self->_vertex_attributes->{$vertex}={};
}


sub _edge2attributes {
  my($self,$u,$v)=@_;
  $self->_edge_attributes->{$u,$v} or $self->_edge_attributes->{$u,$v}={};
}

1;